I am running Linux Mint (a variant of Ubuntu basically). I get the following warning messages:
Worse still. I cannot install packages such as edgeR.
I never had this trouble on my OSX. Has anyone else had experience with problems like this? I tried updating my bioconductor package and that didn't fix it. Never saw this error before.
Code:
> source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1. Warning message: installed directory not writable, cannot update packages 'class', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'
Code:
* installing *source* package ‘edgeR’ ... ** libs g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_cr_adjust.cpp -o R_cr_adjust.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_levenberg.cpp -o R_levenberg.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_one_group.cpp -o R_one_group.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/adj_coxreid.cpp -o core/adj_coxreid.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/glm_levenberg.cpp -o core/glm_levenberg.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/glm_one_group.cpp -o core/glm_one_group.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/interpolator.cpp -o core/interpolator.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/fmm_spline.c -o core/fmm_spline.o g++ -shared -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [edgeR.so] Error 1 ERROR: compilation failed for package ‘edgeR’ * removing ‘/home/hlyates/R/x86_64-pc-linux-gnu-library/3.0/edgeR’ The downloaded source packages are in ‘/tmp/Rtmpu5qpbt/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘edgeR’ had non-zero exit status 2: installed directory not writable, cannot update packages 'class', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'
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